Stool testing is a commonly used for children with autism. It gives us useful information about gut function and the microflora which inhabit it. We are able to gather information about pathogens, yeasts and inflammation along with signs of digestive irregularities. Clinical nutritionists can use this information to infer how these findings might impact the rest of the body.

It is fairly easy to collect a stool sample compared to a blood tests. This is particularly important when working with children with autism. Although, any parent who has tried to collect three samples from their child will tell you it can take some planning and forethought.

Here I want to highlight some of the common findings in the stools of children with autism.


Dysbiosis means that the gut flora are disrupted. There are too little of the right kind, too many of the wrong kind or not enough variety to maintain healthy gut function. This is a common finding in children with autism. Many have bacterial overgrowths that can influence neurological function, for example the clostridia species. Others bacteria, such as low levels of Oxalobacter formigenes, suggest a higher risk of developing oxalate issues. They key thing to remember here is that it is not the presence of certain flora that cause problems but the levels. If there are many then an imbalance is created. None of these bacteria are problematic in smaller amounts, but an overgrowth is a different matter.

Pathogens are often raised in the guts of children with autism. These are bacteria that can take over the gut, causing damage to the gut wall and releasing toxins that can affect physical health and cognitive function.

Surprisingly, I have only seen parasitic infections present in less than 1/5 of the stool tests I’ve reviewed. The lab I use claims that they can detect 90% of parasites through microscopic examination and parasitology enzyme immunology (EIA) tests.


Yeasts overgrowths are a common finding too. Yeasts such as candida species are allowed to flourish during antibiotic use and a diet high in starchy foods will allow them to maintain their hold in the gut. Most stool testing labs will culture the yeasts and then identify the best natural agent to attack it with.


This can be seen by two measures – calprotectin and eosinophil protein X (EPX). Calprotectin is raised in people with inflammatory bowel disease. If just EPX is raised this suggests that there is something in a child’s diet that is causing an immune system response. In both cases care needs to be taken in identifying the right nutritional programme for that child to lower inflammation and improve gut function.

High Faecal Fats:

The last common finding I want to mention here is the presence of high fat in the stool. This tends to indicate a level of maldigestion possibly beginning with a lack of stomach acid secretions. This can affect the absorption of fats and subsequently the fats are found in the stool. This is a key indicator that digestion needs fine tuning and to take a closer look at the possibility of deficiencies in fat soluble nutrients.

I use the GI Effects stool test with Genova Diagnostics for around £344.

If you are interested in running a stool test for yourself or your child. Give me a call on 0121 444 0500 or fill in my contact form and I’ll get back to you.